By Agence France-Presse
Duterte, a charismatic politician known at home for his folksy charm, dropped many of the formal protocols normally associated with visits by a head of government as he took Abe on a tour of his beloved southern home city of Davao.
Abe's day began with a visit to Duterte's "simple home" for a breakfast of sticky rice cakes and mung bean soup, a presidential aide said, with the leaders dining at a wooden table before heading for a look around Duterte's house.
"We also showed him how the president enjoys the comfort of his own bed, including his old and favourite mosquito net," Duterte's aide, Christopher Go, wrote on Facebook alongside a photo of the leaders smiling while standing next to the bed.
The leaders later had a casual meeting at a hotel overlooking the sea, where Duterte was photographed in a checkered shirt and long pants but no socks -- a familiar look for the 71-year-old who takes pride in his informal fashion style.
Abe's next activity saw him standing in front of a stuffed Philippine eagle, the national bird and one of the world's most endangered.
A ceremony saw a two-year-old eagle named Sakura after the famous Japanese cherry blossom.
Abe was given a photo of the eagle, which is kept at a nearby sanctuary, as well as a fluffy toy version draped in indigenous clothing.
Abe, normally blue-suited and politically conservative who nevertheless showed off his fun side last year when he dressed up as video game icon Super Mario at the Rio Olympics' closing ceremony, appeared to enjoy the day.
He smiled and laughed throughout the eagle ceremony, and ended his Davao trip at a Japanese-language school where he was greeted by singing and flag-waving children.
Abe was the first foreign leader to visit the Philippines since Duterte took office just over six months ago.
His two-day trip began on Thursday with a much more formal itinerary in the capital of Manila, where he held meetings with Duterte at the presidential palace.
Abe was also the first head of government to visit Davao, the largest city in the southern Philippines that is 1,500 kilometres (900 miles) from Manila.
Duterte, a longtime mayor of Davao before becoming president, has made developing the southern Philippines a top priority, arguing the region has been neglected by "imperial Manila".
Abe flew from Davao to Australia on Friday afternoon as part of a trip that will include Indonesia and Vietnam.